@@ -84,3 +84,7 @@ and crlmmIllumina() in crlmm-illumina.R)

 2009-04-01 Matt Ritchie - committed version 1.0.67

 * added import statement for normalize.quantiles

+

+2009-04-01 R.Scharpf - committed version 1.0.69

+

+* added a few items to the crlmm TODOs

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.68

+Version: 1.0.69

 Date: 2008-12-30

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

@@ -953,7 +953,6 @@ biasAdj <- function(plateIndex, envir, priorProb){

 	plate <- envir[["plate"]]

 	if(missing(priorProb)) priorProb <- rep(1/4, 4) ##uniform

 	emit <- array(NA, dim=c(nrow(A), ncol(A), 10))##SNPs x sample x 'truth'	

-

 	lA <- log2(A)

 	lB <- log2(B)	

 	X <- cbind(lA, lB)

@@ -995,7 +994,11 @@ biasAdj <- function(plateIndex, envir, priorProb){

 	hemDel <- apply(hemDel, c(1,2), sum)

 	norm <- apply(norm, c(1, 2), sum)

 	amp <- apply(amp, c(1,2), sum)

-

+	total <- hemDel + norm + amp

+	hemDel <- hemDel/total

+	norm <- norm/total

+	amp <- amp/total

+	envir[["posteriorProb"]] <- list(hemDel=hemDel, norm=norm, amp=amp) 

 	tmp <- array(NA, dim=c(nrow(A), ncol(A), 4))

 	tmp[, , 1] <- homDel

 	tmp[, , 2] <- hemDel

@@ -6,6 +6,15 @@

 - Allele plots

 - M v S plots

+R. Scharpf (after next release)

+

+- crlmm should return a SnpSet object with elements A, B, calls, and

+  confs in the assayData when save.it=TRUE.  These objects can be very

+  big, so...  

+

+- crlmm function should have an option to return nothing and write to

+  file a SnpSet object for each chromosome.  This would help the copy

+  number part that runs by chromosome

 #####################################

 ### FOR CNRMA